I am converting an existing desktop application to an Android application, but I am very worried about reverse engineering and stuff like that. For the desktop application, I use Launch4J, but I am unaware of anything that can turn an APK file into native code on Android.

Not an answer (I'm not a dev), but some keywords: Native code is rather rare on Android, but there's the "NDK". For code protection, most devs I've heard using any spoke of something called "ProGuard". Others simply make their code Open Source – which also minimizes the danger of "reverse engineering" ;)
– Izzy♦Aug 28 '14 at 16:28